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fix for a bug deep in the tribble indexing: if you had a single record in the first contig, the second contig's index blocks would point to the wrong file seek location, and you'd see no 

features in that contig. Thanks to Mark for finding this.  I'm not rev'ing the index version (which would cause all indexes to be rebuilt), since this seems like a pretty rare edge case.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3865 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-07-23 18:39:55 +00:00
parent 33090629ea
commit b3fd145161
3 changed files with 5 additions and 7 deletions
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10
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
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@ -35,8 +35,8 @@ import org.broad.tribble.index.IndexFactory;
import org.broad.tribble.index.interval.IntervalIndexCreator;
import org.broad.tribble.index.linear.LinearIndexCreator;
import org.broad.tribble.source.BasicFeatureSource;
import org.broad.tribble.util.LEDataOutputStream;
import org.broad.tribble.util.LEDataStreamUtils;
import org.broad.tribble.util.LittleEndianInputStream;
import org.broad.tribble.util.LittleEndianOutputStream;
import org.broad.tribble.vcf.NameAwareCodec;
import org.broadinstitute.sting.gatk.refdata.tracks.TribbleTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
@ -46,9 +46,7 @@ import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.file.FSLockWithShared;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.*;
import java.util.*;
@ -267,7 +265,7 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
locked = lock.exclusiveLock();
if (locked) {
logger.info("Writing Tribble index to disk for file " + inputFile);
LEDataOutputStream stream = LEDataStreamUtils.createOutputStream(indexFile);
LittleEndianOutputStream stream = new LittleEndianOutputStream(new FileOutputStream(indexFile));
index.write(stream);
stream.close();
}

BIN
settings/repository/org.broad/tribble-124M.jar → settings/repository/org.broad/tribble-129M.jar
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2
settings/repository/org.broad/tribble-124M.xml → settings/repository/org.broad/tribble-129M.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="org.broad" module="tribble" revision="124M" status="integration" publication="201007221854200" />
<info organisation="org.broad" module="tribble" revision="129M" status="integration" publication="201007231854200" />
</ivy-module>